Package | Description |
---|---|
com.compomics.util.experiment.biology.ions |
Experiment classes related to ions.
|
com.compomics.util.experiment.identification.modification |
Additional PSM scoring classes.
|
com.compomics.util.experiment.identification.modification.scores |
PTM scores.
|
com.compomics.util.experiment.identification.psm_scoring |
Main PSM scoring class.
|
com.compomics.util.experiment.identification.psm_scoring.psm_scores |
Main PTM scoring classes.
|
com.compomics.util.experiment.identification.spectrum_annotation |
Classes used for ms2 spectrum annotation.
|
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators |
This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
|
Modifier and Type | Method and Description |
---|---|
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> |
IonFactory.getFragmentIons(Peptide peptide,
SpecificAnnotationParameters specificAnnotationSettings)
This method returns the theoretic ions expected from a peptide.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>> |
ModificationtableContent.getModificationPlotData(Peptide peptide,
Modification modification,
int nMod,
Spectrum spectrum,
AnnotationParameters annotationPreferences,
SpecificAnnotationParameters specificAnnotationPreferences)
Returns the modification plot series in the JFreechart format for one
PSM.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<Modification> modifications,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
double |
PsmScoresEstimator.getDecreasingScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
int scoreIndex)
Scores the match between the given peptide and spectrum using the given
score.
|
double |
PsmScoresEstimator.getScore(Peptide peptide,
Integer peptideCharge,
Spectrum spectrum,
IdentificationParameters identificationParameters,
SpecificAnnotationParameters specificAnnotationPreferences,
PeptideSpectrumAnnotator peptideSpectrumAnnotator,
PsmScore psmScore)
Scores the match between the given peptide and spectrum using the given
score.
|
Modifier and Type | Method and Description |
---|---|
double |
SnrScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the score.
|
double |
HyperScore.getScore(Peptide peptide,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
PeptideSpectrumAnnotator peptideSpectrumAnnotator)
Returns the hyperscore.
|
Modifier and Type | Field and Description |
---|---|
protected SpecificAnnotationParameters |
SpectrumAnnotator.specificAnnotationSettings
If provided, the annotator will only look for the ions included in the
specific annotation settings.
|
Modifier and Type | Method and Description |
---|---|
SpecificAnnotationParameters |
SpecificAnnotationParameters.clone() |
SpecificAnnotationParameters |
AnnotationParameters.getSpecificAnnotationParameters(String spectrumKey,
SpectrumIdentificationAssumption spectrumIdentificationAssumption)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings)
Returns the currently matched ions with the given settings using the intensity filter.
|
abstract ArrayList<IonMatch> |
SpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter)
Returns the currently matched ions with the given settings.
|
protected HashMap<Integer,ArrayList<Ion>> |
SpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings)
Returns the expected ions in a map indexed by the possible charges.
|
protected ArrayList<IonMatch> |
SpectrumAnnotator.matchPeak(SpecificAnnotationParameters specificAnnotationSettings,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak.
|
Modifier and Type | Method and Description |
---|---|
Map<Integer,ArrayList<IonMatch>> |
PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the ion matches corresponding to fragment ions indexed by amino
acid number in the sequence.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getCurrentAnnotation(Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean useIntensityFilter) |
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag)
Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
|
ArrayList<IonMatch> |
TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Tag tag,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
java.util.stream.Stream<IonMatch> |
PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
Spectrum spectrum,
Peptide peptide,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
ArrayList<IonMatch> |
PeptideSpectrumAnnotator.matchPeak(Peptide peptide,
SpecificAnnotationParameters specificAnnotationSettings,
Peak peak)
This method matches the potential fragment ions of a given peptide with a
given peak according to the annotation settings.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons,
int precursorCharge,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
void |
PeptideSpectrumAnnotator.setPeptide(Peptide peptide,
int precursorCharge,
SpecificAnnotationParameters specificAnnotationSettings)
Sets a new peptide to annotate.
|
Copyright © 2018. All rights reserved.